Skip to content

Commit 0e0c62f

Browse files
akleemanakleeman
authored
Isolate Cereal (#153)
* Switch Prior from being a pointer to an abstract class, to being a variant. * Move all serialization methods into the cereal directory * Remove unused files * Split the serialization includes apart, this avoids needing to include all of albatross if you only want serialization of one part. For example, #include <albatross/Core> would only need: #include <albatross/serialize/Core> without this including albatross/Serialization would require including everything (since some of the types would not have been defined for the `serialize()` methods. * Add similar includes for the utils which are commonly used on their own * Seth's changes * Joseph's comments * Change relative paths to include paths
1 parent f680471 commit 0e0c62f

Some content is hidden

Large Commits have some content hidden by default. Use the searchbox below for content that may be hidden.

64 files changed

+981
-618
lines changed

‎examples/temperature_example/temperature_example.cc‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -62,7 +62,7 @@ int main(int argc, char *argv[]) {
6262
auto covariance = elevation_scaled_mean + noise + spatial_cov;
6363
auto model = gp_from_covariance(covariance);
6464

65-
model.set_param("sigma_exponential", {1., std::make_shared<FixedPrior>()});
65+
model.set_param("sigma_exponential", {1., FixedPrior()});
6666

6767
// These parameters are that came from tuning the model to the leave
6868
// one out negative log likelihood. which can be done like this:

‎examples/temperature_example/temperature_example_utils.h‎

Lines changed: 3 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -68,10 +68,9 @@ class StationDistance : public DistanceMetricType {
6868
class ElevationScalingFunction : public albatross::ScalingFunction {
6969
public:
7070
ElevationScalingFunction(double center = 1000., double factor = 3.5 / 300) {
71-
this->params_["elevation_scaling_center"] = {
72-
center, std::make_shared<UniformPrior>(0., 5000.)};
73-
this->params_["elevation_scaling_factor"] = {
74-
factor, std::make_shared<PositivePrior>()};
71+
this->params_["elevation_scaling_center"] = {center,
72+
UniformPrior(0., 5000.)};
73+
this->params_["elevation_scaling_factor"] = {factor, PositivePrior()};
7574
};
7675

7776
std::string get_name() const { return "elevation_scaled"; }

‎include/albatross/Common‎

Lines changed: 6 additions & 16 deletions
Original file line numberDiff line numberDiff line change
@@ -13,14 +13,6 @@
1313
#ifndef ALBATROSS_COMMON_H
1414
#define ALBATROSS_COMMON_H
1515

16-
#include <cereal/cereal.hpp>
17-
#include <cereal/archives/binary.hpp>
18-
#include <cereal/archives/json.hpp>
19-
#include <cereal/archives/xml.hpp>
20-
#include <cereal/types/polymorphic.hpp>
21-
#include <cereal/types/map.hpp>
22-
#include <cereal/types/vector.hpp>
23-
2416
#include <gzip/compress.hpp>
2517
#include <gzip/decompress.hpp>
2618

@@ -32,6 +24,7 @@
3224
#include <math.h>
3325
#include <iomanip>
3426
#include <map>
27+
#include <set>
3528
#include <string>
3629
#include <iostream>
3730
#include <unordered_map>
@@ -41,15 +34,12 @@
4134
#include <numeric>
4235
#include <random>
4336

44-
#include "src/core/declarations.hpp"
37+
#include <albatross/src/core/declarations.hpp>
4538

46-
#include "src/details/traits.hpp"
47-
#include "src/details/has_any_macros.hpp"
48-
#include "src/details/error_handling.hpp"
39+
#include <albatross/src/details/traits.hpp>
40+
#include <albatross/src/details/has_any_macros.hpp>
41+
#include <albatross/src/details/error_handling.hpp>
4942

50-
#include "src/utils/map_utils.hpp"
51-
#include "src/cereal/eigen.hpp"
52-
#include "src/cereal/traits.hpp"
53-
#include "src/cereal/variant.hpp"
43+
#include <albatross/src/utils/map_utils.hpp>
5444

5545
#endif

‎include/albatross/Core‎

Lines changed: 9 additions & 9 deletions
Original file line numberDiff line numberDiff line change
@@ -17,14 +17,14 @@
1717

1818
#include <type_traits>
1919

20-
#include "src/core/declarations.hpp"
21-
#include "src/core/indexing.hpp"
22-
#include "src/core/traits.hpp"
23-
#include "src/core/priors.hpp"
24-
#include "src/core/parameter_handling_mixin.hpp"
25-
#include "src/core/parameter_macros.hpp"
26-
#include "src/core/fit_model.hpp"
27-
#include "src/core/prediction.hpp"
28-
#include "src/core/model.hpp"
20+
#include <albatross/src/core/declarations.hpp>
21+
#include <albatross/src/core/indexing.hpp>
22+
#include <albatross/src/core/traits.hpp>
23+
#include <albatross/src/core/priors.hpp>
24+
#include <albatross/src/core/parameter_handling_mixin.hpp>
25+
#include <albatross/src/core/parameter_macros.hpp>
26+
#include <albatross/src/core/fit_model.hpp>
27+
#include <albatross/src/core/prediction.hpp>
28+
#include <albatross/src/core/model.hpp>
2929

3030
#endif

‎include/albatross/CovarianceFunctions‎

Lines changed: 15 additions & 15 deletions
Original file line numberDiff line numberDiff line change
@@ -15,21 +15,21 @@
1515

1616
#include "Common"
1717

18-
#include "src/core/declarations.hpp"
19-
#include "src/core/traits.hpp"
20-
#include "src/core/priors.hpp"
21-
#include "src/core/parameter_handling_mixin.hpp"
22-
#include "src/core/parameter_macros.hpp"
18+
#include <albatross/src/core/declarations.hpp>
19+
#include <albatross/src/core/traits.hpp>
20+
#include <albatross/src/core/priors.hpp>
21+
#include <albatross/src/core/parameter_handling_mixin.hpp>
22+
#include <albatross/src/core/parameter_macros.hpp>
2323

24-
#include "src/covariance_functions/traits.hpp"
25-
#include "src/covariance_functions/callers.hpp"
26-
#include "src/covariance_functions/covariance_function.hpp"
27-
#include "src/covariance_functions/call_trace.hpp"
28-
#include "src/covariance_functions/measurement.hpp"
29-
#include "src/covariance_functions/distance_metrics.hpp"
30-
#include "src/covariance_functions/noise.hpp"
31-
#include "src/covariance_functions/polynomials.hpp"
32-
#include "src/covariance_functions/radial.hpp"
33-
#include "src/covariance_functions/scaling_function.hpp"
24+
#include <albatross/src/covariance_functions/traits.hpp>
25+
#include <albatross/src/covariance_functions/callers.hpp>
26+
#include <albatross/src/covariance_functions/covariance_function.hpp>
27+
#include <albatross/src/covariance_functions/call_trace.hpp>
28+
#include <albatross/src/covariance_functions/measurement.hpp>
29+
#include <albatross/src/covariance_functions/distance_metrics.hpp>
30+
#include <albatross/src/covariance_functions/noise.hpp>
31+
#include <albatross/src/covariance_functions/polynomials.hpp>
32+
#include <albatross/src/covariance_functions/radial.hpp>
33+
#include <albatross/src/covariance_functions/scaling_function.hpp>
3434

3535
#endif

‎include/albatross/Dataset‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -15,7 +15,7 @@
1515

1616
#include "Distribution"
1717

18-
#include "src/core/concatenate.hpp"
19-
#include "src/core/dataset.hpp"
18+
#include <albatross/src/core/concatenate.hpp>
19+
#include <albatross/src/core/dataset.hpp>
2020

2121
#endif

‎include/albatross/Distribution‎

Lines changed: 3 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -15,11 +15,8 @@
1515

1616
#include "Common"
1717

18-
#include "src/cereal/traits.hpp"
19-
#include "src/eigen/serializable_diagonal_matrix.hpp"
20-
21-
#include "src/core/declarations.hpp"
22-
#include "src/core/indexing.hpp"
23-
#include "src/core/distribution.hpp"
18+
#include <albatross/src/core/declarations.hpp>
19+
#include <albatross/src/core/indexing.hpp>
20+
#include <albatross/src/core/distribution.hpp>
2421

2522
#endif

‎include/albatross/Evaluation‎

Lines changed: 9 additions & 9 deletions
Original file line numberDiff line numberDiff line change
@@ -15,14 +15,14 @@
1515

1616
#include "Core"
1717

18-
#include "src/evaluation/likelihood.hpp"
19-
#include "src/evaluation/differential_entropy.hpp"
20-
#include "src/covariance_functions/traits.hpp"
21-
#include "src/evaluation/traits.hpp"
22-
#include "src/evaluation/folds.hpp"
23-
#include "src/evaluation/prediction_metrics.hpp"
24-
#include "src/evaluation/model_metrics.hpp"
25-
#include "src/evaluation/cross_validation_utils.hpp"
26-
#include "src/evaluation/cross_validation.hpp"
18+
#include <albatross/src/evaluation/likelihood.hpp>
19+
#include <albatross/src/evaluation/differential_entropy.hpp>
20+
#include <albatross/src/covariance_functions/traits.hpp>
21+
#include <albatross/src/evaluation/traits.hpp>
22+
#include <albatross/src/evaluation/folds.hpp>
23+
#include <albatross/src/evaluation/prediction_metrics.hpp>
24+
#include <albatross/src/evaluation/model_metrics.hpp>
25+
#include <albatross/src/evaluation/cross_validation_utils.hpp>
26+
#include <albatross/src/evaluation/cross_validation.hpp>
2727

2828
#endif

‎include/albatross/GP‎

Lines changed: 5 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -16,10 +16,10 @@
1616
#include "Core"
1717
#include "CovarianceFunctions"
1818

19-
#include "src/evaluation/likelihood.hpp"
20-
#include "src/eigen/serializable_ldlt.hpp"
21-
#include "src/utils/block_utils.hpp"
22-
#include "src/covariance_functions/representations.hpp"
23-
#include "src/models/gp.hpp"
19+
#include <albatross/src/evaluation/likelihood.hpp>
20+
#include <albatross/src/eigen/serializable_ldlt.hpp>
21+
#include <albatross/src/utils/block_utils.hpp>
22+
#include <albatross/src/covariance_functions/representations.hpp>
23+
#include <albatross/src/models/gp.hpp>
2424

2525
#endif

‎include/albatross/LeastSquares‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -15,6 +15,6 @@
1515

1616
#include "Core"
1717

18-
#include "src/models/least_squares.hpp"
18+
#include <albatross/src/models/least_squares.hpp>
1919

2020
#endif

0 commit comments

Comments
 (0)